Python Compound.get_bitmap_fingerprint Examples

Example #1

def generate_fingerprint(smiles):
    if smiles:
        compound = Compound(compound_string=smiles, identifier_type='smiles', suppress_hydrogens=True)
        fingerprint = compound.get_bitmap_fingerprint()
        fp = {x for x in str(fingerprint)[1:-1].split(', ')}
        return list(fp)
    else:
        return []

Example #2

def generate_fingerprint(smiles, compound_id, main_label, qid):
    if smiles:
        compound = Compound(compound_string=smiles,
                            identifier_type='smiles',
                            suppress_hydrogens=True)
        fingerprint = compound.get_bitmap_fingerprint()
        fp = {x for x in str(fingerprint)[1:-1].split(', ')}

        # if only compound id is set as a label, try to set something more useful
        if compound_id in compound_id_fp_map:
            sim_item = compound_id_fp_map[compound_id]
            if sim_item[1] == compound_id:
                sim_item[1] = main_label
        else:
            compound_id_fp_map.update(
                {compound_id: (compound_id, main_label, qid, fp)})

        return list(fp)
    else:
        return []